Walkthrough on GUI based tilt series alignment

Dynamo includes a package for automated aligned and reconstruction of tilt series. This walkthrough guides you through the steps on how to use it with a GUI. A different page in this wiki

Data

We have prepared version a tilt series from the EMPIAR entry [XXXX]

/html/w/doc/data/hiv/align/b001ts001.mrc

In this binned version, the pixel size is 2'7 Angstrom (original was 1.35, this is bin level 1 in Dynamo)

Creating an alignment workflow

The basic function for invoking the GUI is dtsa (short form of dynamo_tilt_series_alignment;

 dtsa('folder','firstAlign);

The data for the workflow (tilt series, angles) could have been introduced directly when creating the workflow, we however will introduce each item explicitly in this walkthrough.

GUI description

The GUI guides of the process of creating and editing a set of "working markers" (in the areas of detection, reindexing and refinement), and then using them to create aligned stacks (alignment tab), analyse and correct their CTF (through wrappers to ctfffind4 and imod) and then create reconstructions.

Settings

Acqusition settings

Here you enter pixel size (2.7 Angstroms), Cs (2.2), nominal defocus (-4.0 microns, used if the CTF area is connected).

Controls

markers GUI

The icon of the markers GUI allows you to check the position of the working markers in the micrograph. If you want to make editions of the GUI permanent, you need to save the current markers.

Occupancy plot

Shows a scheme of which markers are present in which tilt numbers.

Gold bead gallery

Crops the gold beads currently contained in the working markers and shows them as a gallery.

Execution Areas

The GUI is divided in five areas, which are sets of steps that can be executed sequentially. Sequential execution is the natural way of proceeding; but steps can be visited in any order, i.e., a step can be reexecuted in a later moment after updating its information.

Steps

Steps needs to be open (letters in grey) in order to be executed. They become open when the input they require gets computed and stored during execution of the workflow. When a step is under execution, its pushbutton becomes green.

Step Toolbox

The tool icon can be secondary clicked and will provide a popup menu with specific tools for each steps and some common one. The common ones are handles to inspect and list the items that are needed (input items) or generated (output items) by the step. The View provides tools specific for visualisation of results of the step.

Entering the data

The minimal data to initiate. w work

• tilt series matrix.
• tilt angles.
• discarded tilt angles

Discarded tilt angles

Tilt angles to be discarded can be selected directly with the dmarkers GUI using the x and shift + x buttons.

The areas in the alignment task

Detection

Visualization matrix

This step just creates a binned version of the tilt series stack to accelerate visualizations that will be invoked in a later point.

CTF

In this GUI CTF estimation and correction are delegated to CTFFIND4 and Imod's ctfphaseflip programs respectively.

Reconstruction

Full sized reconstruction

File:ImagesWiki/imagesForWiki/alignGUI creatingAWorkflow.png

creating a workflow

File:ImagesWiki/imagesForWiki/alignGUI inputWorkflowParameters.png

input workflow parameters

File:ImagesWiki/imagesForWiki/alignGUI creationOfWorkflowGUITakesSomeSeconds.png

creation of workflow GUI takes some seconds

File:ImagesWiki/imagesForWiki/alignGUI alignmentGUIBeforeCompletionOfAnyStep.png

alignment GUI before completion of any step

File:ImagesWiki/imagesForWiki/alignGUI passingTheCursorOnTheGUIElementsShowsAHelpElement.png

passing the cursor on the GUI elements shows a help element

File:ImagesWiki/imagesForWiki/alignGUI completedStepsBecomeBoldFontSize.png

completed steps become bold font size

File:ImagesWiki/imagesForWiki/alignGUI thePlusIconAtCornerShowsTheValuesOfTheParametersOfAGivenStep.png

the plus icon at corner shows the values of the parameters of a given step

File:ImagesWiki/imagesForWiki/alignGUI openTomoshowOnTheFullSizedMatrixToCheckTheSizeOfAGoldBead.png

open tomoshow on the full sized matrix to check the size of a gold bead

File:ImagesWiki/imagesForWiki/alignGUI theRulerToolAllowsToMeasureInPixelsTheDiameterOfAGoldBead.png

the ruler tool allows to measure in pixels the diameter of a gold bead

File:ImagesWiki/imagesForWiki/alignGUI secondaryClickInTheViewPanelOpensAMenuToAccessTheDifferentResultsOfAStep.png

secondary click in the view panel opens a menu to access the different results of a step

File:ImagesWiki/imagesForWiki/alignGUI markerSetsCanBeViewedAsCloudOfPoints.png

marker sets can be viewed as cloud of points